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Methods in Molecular Biology (Clifton,... 2022The aim in microarray data analysis is to discover patterns of gene expression and to identify similar genes. Simply comparing new gene sequences to known DNA sequences...
The aim in microarray data analysis is to discover patterns of gene expression and to identify similar genes. Simply comparing new gene sequences to known DNA sequences often does not reveal the function of a new gene; thus, more sophisticated techniques are in order. Nowadays, data mining techniques, and in particular the clustering process, play an important role in bioinformatics. To analyze vast amounts of data can be difficult; thus, a way to cluster similar data is needed. This chapter is devoted to illustrate the general data mining approach used in microarray data analysis, combining clustering, alignment and similarity, and to highlight a novel similarity measure capable of capturing hidden correlations between data.
Topics: Algorithms; Cluster Analysis; Computational Biology; Gene Expression Profiling; Microarray Analysis; Oligonucleotide Array Sequence Analysis
PubMed: 34902131
DOI: 10.1007/978-1-0716-1839-4_14 -
Journal of Pharmaceutical and... Jan 2016Metallothioneins (MTs), low molecular mass cysteine-rich proteins, which are able to bind up to 20 monovalent and up to 7 divalent heavy metal ions are widely studied... (Review)
Review
Metallothioneins (MTs), low molecular mass cysteine-rich proteins, which are able to bind up to 20 monovalent and up to 7 divalent heavy metal ions are widely studied due to their functions in detoxification of metals, scavenging free radicals and cells protection against the oxidative stress. It was found that the loss of the protective effects of MT leads to an escalation of pathogenic processes and carcinogenesis. The most extensive area is MTs expression for oncological applications, where the information about gene patterns is helpful for the identification biological function, resistance to drugs and creating the correct chemotherapy. In other medical applications the effect of oxidative stress to cell lines exposed to heavy metals and hydrogen peroxide is studied as well as influence of drugs and cytokines on MTs expression and MTs expression in the adipose tissue. The precise detection of low metallothionein concentrations and its isoforms is necessary to understand the connection between quantity and isoforms of MTs to size, localization and type of cancer. This information is necessary for well-timed therapy and increase the chance to survival. Microarray chips appear as good possibility for finding all information about expression of MTs genes and isoforms not only in cancer, but also in other diseases, especially diabetes, obesity, cardiovascular diseases, ageing, osteoporosis, psychiatric disorders and as the effects of toxic drugs and pollutants, which is discussed in this review.
Topics: Animals; Humans; Metallothionein; Microarray Analysis; Neoplasms; Oxidative Stress
PubMed: 26454339
DOI: 10.1016/j.jpba.2015.09.031 -
Proteomics. Clinical Applications Jan 2023Although several effective treatment modalities have been developed for cancers, the morbidity and mortality associated with cancer continues to increase every year. As... (Review)
Review
Although several effective treatment modalities have been developed for cancers, the morbidity and mortality associated with cancer continues to increase every year. As one of the most exciting emerging technologies, protein microarrays represent a powerful tool in the field of cancer research because of their advantages such as high throughput, small sample usage, more flexibility, high sensitivity and direct readout of results. In this review, we focus on the research progress in four types of protein microarrays (proteome microarray, antibody microarray, lectin microarray and reversed protein array) with emphasis on their application in cancer research. Finally, we discuss the current challenges faced by protein microarrays and directions for future developments. We firmly believe that this novel systems biology research tool holds immense potential in cancer research and will become an irreplaceable tool in this field.
Topics: Protein Array Analysis; Microarray Analysis; Proteome; Lectins; Neoplasms
PubMed: 36316278
DOI: 10.1002/prca.202200036 -
Journal of Visualized Experiments : JoVE Sep 2023Microarray polymer profiling (MAPP) is a robust and reproducible approach to systematically determine the composition and relative abundance of glycans and...
Microarray polymer profiling (MAPP) is a robust and reproducible approach to systematically determine the composition and relative abundance of glycans and glycoconjugates within a variety of biological samples, including plant and algal tissues, food materials, and human, animal, and microbial samples. Microarray technology underpins the efficacy of this method by providing a miniaturized, high-throughput screening platform, allowing thousands of interactions between glycans and highly specific glycan-directed molecular probes to be characterized concomitantly, using only small amounts of analytes. Constituent glycans are chemically and enzymatically fractionated, before being sequentially extracted from the sample and directly immobilized onto nitrocellulose membranes. The glycan composition is determined by the attachment of specific glycan-recognizing molecular probes to the extorted and printed molecules. MAPP is complementary to conventional glycan analysis techniques, such as monosaccharide and linkage analysis and mass spectrometry. However, glycan-recognizing molecular probes provide insight into the structural configurations of glycans, which can aid in elucidating biological interactions and functional roles.
Topics: Animals; Humans; Microarray Analysis; Polysaccharides; Glycoconjugates; Mass Spectrometry; Molecular Probes; Plants
PubMed: 37843288
DOI: 10.3791/65443 -
Annual Review of Analytical Chemistry... 2015DNA/RNA and protein microarrays have proven their outstanding bioanalytical performance throughout the past decades, given the unprecedented level of parallelization by... (Review)
Review
DNA/RNA and protein microarrays have proven their outstanding bioanalytical performance throughout the past decades, given the unprecedented level of parallelization by which molecular recognition assays can be performed and analyzed. Cell microarrays (CMAs) make use of similar construction principles. They are applied to profile a given cell population with respect to the expression of specific molecular markers and also to measure functional cell responses to drugs and chemicals. This review focuses on the use of cell-based microarrays for assessing the cytotoxicity of drugs, toxins, or chemicals in general. It also summarizes CMA construction principles with respect to the cell types that are used for such microarrays, the readout parameters to assess toxicity, and the various formats that have been established and applied. The review ends with a critical comparison of CMAs and well-established microtiter plate (MTP) approaches.
Topics: Animals; Biomarkers; Cell Physiological Phenomena; Dose-Response Relationship, Drug; Humans; Microarray Analysis; Toxicology
PubMed: 26077916
DOI: 10.1146/annurev-anchem-071213-020051 -
Methods in Molecular Biology (Clifton,... 2019A receiver operating characteristic (ROC) curve is a graphical plot that illustrates the diagnostic ability of a binary classifier as a function of its discrimination... (Review)
Review
A receiver operating characteristic (ROC) curve is a graphical plot that illustrates the diagnostic ability of a binary classifier as a function of its discrimination threshold. This chapter is an overview on the use of ROC curves for microarray data. The notion of ROC curve and its motivation is introduced in Subheading 1. Relevant scientific contributions concerning the use of ROC curves for microarray data are briefly reviewed in Subheading 2. The special case with covariates is considered in Subheading 3. Two relevant aspects are reviewed in this section: the use of LASSO techniques for selecting and combining relevant markers and how to correct for multiple testing when a large number of markers are available. Finally, some conclusions are included.
Topics: Algorithms; Microarray Analysis; ROC Curve
PubMed: 31115892
DOI: 10.1007/978-1-4939-9442-7_11 -
FEBS Letters Dec 2018The neoglycolipid (NGL) technology is the basis of a state-of-the-art oligosaccharide microarray system, which we offer for screening analyses to the broad scientific... (Review)
Review
The neoglycolipid (NGL) technology is the basis of a state-of-the-art oligosaccharide microarray system, which we offer for screening analyses to the broad scientific community. We review here the sequential development of the technology and its power in pinpointing and isolating naturally occurring ligands for glycan-binding proteins (GBPs) within glycan populations. We highlight our Designer Array approach and Beam Search Array approach for generating natural glycome arrays to identify novel ligands of biological relevance. These two microarray approaches have been applied for assignments of ligands or antigens on glucan polysaccharides for effector proteins of the immune system (Dectin-1, DC-SIGN and DC-SIGNR) and carbohydrate-binding modules (CBMs) on bacterial hydrolases. We also discuss here the more recent applications to elucidate the structure of a prostate cancer- associated antigen F77 and identify ligands for adhesins of two rotaviruses, P[10] and P[19], expressed on an epithelial mucin glycoprotein.
Topics: Animals; Glucans; Glycolipids; Glycomics; Humans; Lectins, C-Type; Ligands; Microarray Analysis; Oligosaccharides
PubMed: 30074246
DOI: 10.1002/1873-3468.13217 -
Cold Spring Harbor Protocols Oct 2016Protein microarrays have emerged as a powerful tool for the scientific community, and their greatest advantage lies in the fact that thousands of reactions can be... (Review)
Review
Protein microarrays have emerged as a powerful tool for the scientific community, and their greatest advantage lies in the fact that thousands of reactions can be performed in a parallel and unbiased manner. The first high-density protein microarray, dubbed the "yeast proteome array," consisted of approximately 5800 full-length yeast proteins and was initially used to identify protein-lipid interactions. Further assays were subsequently developed to allow measurement of protein-DNA, protein-RNA, and protein-protein interactions, as well as four well-known posttranslational modifications: phosphorylation, acetylation, ubiquitylation, and SUMOylation. In this introduction, we describe the advent of high-density protein microarrays, as well as current methods for assessing a wide variety of protein interactions and posttranslational modifications.
Topics: Microarray Analysis; Protein Array Analysis
PubMed: 27698245
DOI: 10.1101/pdb.top081471 -
Human Reproduction Update Nov 2020The placenta is the active interface between mother and foetus, bearing the molecular marks of rapid development and exposures in utero. The placenta is routinely... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
The placenta is the active interface between mother and foetus, bearing the molecular marks of rapid development and exposures in utero. The placenta is routinely discarded at delivery, providing a valuable resource to explore maternal-offspring health and disease in pregnancy. Genome-wide profiling of the human placental transcriptome provides an unbiased approach to study normal maternal-placental-foetal physiology and pathologies.
OBJECTIVE AND RATIONALE
To date, many studies have examined the human placental transcriptome, but often within a narrow focus. This review aims to provide a comprehensive overview of human placental transcriptome studies, encompassing those from the cellular to tissue levels and contextualize current findings from a broader perspective. We have consolidated studies into overarching themes, summarized key research findings and addressed important considerations in study design, as a means to promote wider data sharing and support larger meta-analysis of already available data and greater collaboration between researchers in order to fully capitalize on the potential of transcript profiling in future studies.
SEARCH METHODS
The PubMed database, National Center for Biotechnology Information and European Bioinformatics Institute dataset repositories were searched, to identify all relevant human studies using 'placenta', 'decidua', 'trophoblast', 'transcriptome', 'microarray' and 'RNA sequencing' as search terms until May 2019. Additional studies were found from bibliographies of identified studies.
OUTCOMES
The 179 identified studies were classifiable into four broad themes: healthy placental development, pregnancy complications, exposures during pregnancy and in vitro placental cultures. The median sample size was 13 (interquartile range 8-29). Transcriptome studies prior to 2015 were predominantly performed using microarrays, while RNA sequencing became the preferred choice in more recent studies. Development of fluidics technology, combined with RNA sequencing, has enabled transcript profiles to be generated of single cells throughout pregnancy, in contrast to previous studies relying on isolated cells. There are several key study aspects, such as sample selection criteria, sample processing and data analysis methods that may represent pitfalls and limitations, which need to be carefully considered as they influence interpretation of findings and conclusions. Furthermore, several areas of growing importance, such as maternal mental health and maternal obesity are understudied and the profiling of placentas from these conditions should be prioritized.
WIDER IMPLICATIONS
Integrative analysis of placental transcriptomics with other 'omics' (methylome, proteome and metabolome) and linkage with future outcomes from longitudinal studies is crucial in enhancing knowledge of healthy placental development and function, and in enabling the underlying causal mechanisms of pregnancy complications to be identified. Such understanding could help in predicting risk of future adversity and in designing interventions that can improve the health outcomes of both mothers and their offspring. Wider collaboration and sharing of placental transcriptome data, overcoming the challenges in obtaining sufficient numbers of quality samples with well-defined clinical characteristics, and dedication of resources to understudied areas of pregnancy will undoubtedly help drive the field forward.
Topics: Female; Gene Expression Profiling; Humans; Microarray Analysis; Placenta; Placentation; Pregnancy; Pregnancy Complications; Pregnancy Trimester, First; Trophoblasts
PubMed: 33043357
DOI: 10.1093/humupd/dmaa028 -
Expert Review of Molecular Diagnostics 2015Methods to detect immunolabeled molecules at increasingly higher resolutions, even when present at low levels, are revolutionizing immunohistochemistry (IHC). These... (Review)
Review
Methods to detect immunolabeled molecules at increasingly higher resolutions, even when present at low levels, are revolutionizing immunohistochemistry (IHC). These technologies can be valuable for the management and examination of rare patient tissue specimens, and for improved accuracy of early disease detection. The purpose of this article is to highlight recent multiplexing methods that are candidates for more prevalent use in clinical research and potential translation to the clinic. Multiplex IHC methods, which permit identification of at least 3 and up to 30 discrete antigens, have been divided into whole-section staining and spatially-patterned staining categories. Associated signal enhancement technologies that can enhance performance and throughput of multiplex IHC assays are also discussed. Each multiplex IHC technique, detailed herein, is associated with several advantages as well as tradeoffs that must be taken into consideration for proper evaluation and use of the methods.
Topics: Humans; Immunohistochemistry; Microarray Analysis; Microfluidics
PubMed: 26289603
DOI: 10.1586/14737159.2015.1069182